2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f95cf49907cc/ Changeset: f95cf49907cc User: jmchilton Date: 2014-05-14 21:08:03 Summary: Bugfix: Annotation, tags on collections update looking in old location. Moved to collection instances instead of collections a little before PR opened. Affected #: 1 file diff -r 6fecbad49afd69beebb55fb8a9b83ecae29af723 -r f95cf49907cca1c57a2fad9738e66c9aa5078fb9 lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -138,10 +138,10 @@ changed = dataset_collection_instance.set_from_dict( new_data ) # the rest (often involving the trans) - do here if 'annotation' in new_data.keys() and trans.get_user(): - dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance.collection, new_data[ 'annotation' ] ) + dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] ) changed[ 'annotation' ] = new_data[ 'annotation' ] if 'tags' in new_data.keys() and trans.get_user(): - self.set_tags_from_list( trans, dataset_collection_instance.collection, new_data[ 'tags' ], user=trans.user ) + self.set_tags_from_list( trans, dataset_collection_instance, new_data[ 'tags' ], user=trans.user ) if changed.keys(): trans.sa_session.flush() https://bitbucket.org/galaxy/galaxy-central/commits/c0832d30e315/ Changeset: c0832d30e315 User: jmchilton Date: 2014-05-14 21:08:56 Summary: Merge. Affected #: 1 file diff -r f95cf49907cca1c57a2fad9738e66c9aa5078fb9 -r c0832d30e315c24dcc2cf23918e4b0bd7b30ba56 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -470,7 +470,7 @@ if index is not None: tool_dependency = tool_dependencies[ index ] tool_dependency, proceed_with_install, action_elem_tuples = \ - tag_manager.process_tag_set( trans.app, + tag_manager.process_tag_set( self.app, tool_shed_repository, tool_dependency, elem, @@ -480,7 +480,7 @@ tool_dependency_db_records=tool_dependencies ) if proceed_with_install: try: - tool_dependency = install_manager.install_package( trans.app, + tool_dependency = install_manager.install_package( self.app, elem, tool_shed_repository, tool_dependencies=tool_dependencies, @@ -493,7 +493,7 @@ # Since there was an installation error, update the tool dependency status to Error. The # remove_installation_path option must be left False here. tool_dependency = \ - tool_dependency_util.handle_tool_dependency_installation_error( trans.app, + tool_dependency_util.handle_tool_dependency_installation_error( self.app, tool_dependency, error_message, remove_installation_path=False ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.